Methods and systems for variant detection

ABSTRACT

In one exemplary embodiment, a method for detecting variants in electropherogram data is provided. The method includes receiving electropherogram data from an instrument and analyzing the electropherogram data to identify mixed bases in the electropherogram data. The method further includes identifying features within the electropherogram data indicative of errors and validating the identified mixed bases. Then the method includes determining variants in the electropherogram data based on the validated mixed bases.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of priority of U.S. ProvisionalPatent Application No. 62/148,049 filed on Apr. 15, 2015, which isincorporated herein in its entirety by reference.

BACKGROUND

Technology invented by Fred Sanger has provided the mainstay ofsequencing approaches since its inception in 1977, culminating with therelease of the Human Genome sequence in 2000 by Human Genome Sciences.Sanger sequencing remains a valuable and viable research tool, but thechallenge of interpreting instrument signals to produce high qualitybiological indication remain.

Basic operation of the Sanger sequencing equipment produces anelectropherogram, a line plot with four traces that traversehorizontally and whose vertical axis records the amplitudes that reflectthe level of detection of the four measured genomic bases: G, A, T, C.Progress along the horizontal position records regular digitized samplesas the sample medium flows through the detection column, carrying withit the genomic (DNA) content. With high-quality traces, the centralregion of the electropherogram shows sequence of well-formed (Gaussian)peaks which are evenly spaced and have consistent amplitude,well-modulated above a low murmur of background noise. In some cases,two peaks will rise simultaneously and typically to a lower height thannormal. This reports a mixed-base observation.

The ends of these traces record the initial introduction of the sampleand the conclusion of the sample and are virtually always of lowerquality, having irregular cadence and irregular and frequently loweredamplitude, and higher noise background. In many cases the peaks are nolonger Gaussian in shape and may have overlapping regions. Qualitytrimming is generally applied to the traces to remove these low-qualityregions, however it is often a compromise between preserving sequenceand rejecting noise.

Low quality traces can occur due to sample contamination, low-qualityprimers, and many other experimental conditions. These can result inirregularities in otherwise high quality traces. Ink blobs are acharacteristic of an irregularity and result in hugely exaggerated peakswhich may span multiple underlying high-quality peaks.

Many researchers continue to trust expert human inspection of Sangerelectropherograms for interpretation rather than trust to automatedprocessing. The many characteristics of the electropherograms are hardto characterize algorithmically without a large body of highly qualifieddata to tune and develop the algorithms.

Humans are diploid organisms, meaning that we have two copies of eachgene in our chromosome. In many cases these copies are heterozygous, orgiving two different alleles of the same genes. With Sanger sequencingthe sequence reflects this heterozygous condition with a combination ofbase values at the differentiating positions that is one allele may havean “A” base while one allele may have a “C” base, and this isrepresented as the mixed-base “M”.

A goal of genomics analysis is to recover the true sequence of bothalleles in the heterozygous case from Sanger sequencing, however theinformation available at secondary analysis is inadequate for accurateassignment of multiple heterozygous observations to alleles.Additionally, many mixed-base observations are the result of instrumentnoise and not true biological variation. The predominance of algorithmsdo not provide mechanism to accurately align mixed-base sequences to areference sequence.

SUMMARY

In one exemplary embodiment, a method for detecting variants inelectropherogram data is provided. The method includes receivingelectropherogram data from an instrument and analyzing theelectropherogram data to identify mixed bases in the electropherogramdata. The method further includes identifying features within theelectropherogram data indicative of errors and validating the identifiedmixed bases. Then the method includes determining variants in theelectropherogram data based on the validated mixed bases.

DESCRIPTION OF THE FIGURES

FIG. 1 illustrates a method of analyzing mixed bases according tovarious embodiments described herein;

FIG. 2 illustrates a method of detecting variants according to variousembodiments described herein;

FIG. 3 illustrates a base compatibility matrix according to variousembodiments described herein;

FIG. 4 illustrates a method of trace analysis according to variousembodiments described herein;

FIG. 5 illustrates various reference frames according to variousembodiments described herein;

FIG. 6 illustrates a region of consideration according to variousembodiments described herein;

FIG. 7 illustrates another region of consideration according to variousembodiments described herein;

FIG. 8 illustrates an exemplary electropherogram according to variousembodiments described herein;

FIG. 9 illustrates an example of a mixed base report according tovarious embodiments described herein;

FIG. 10 illustrates an exemplary electropherogram characteristic thatwill be detected by the peak detection module according to variousembodiments described herein;

FIG. 11 illustrates yet another example of an electropherogramcharacteristic that will be detected by the peak detection moduleaccording to various embodiments described herein;

FIG. 12 illustrates yet another example of an electropherogramcharacteristic that will be detected by the peak detection moduleaccording to various embodiments described herein;

FIG. 13 illustrates yet another example of an electropherogramcharacteristic that will be detected by the peak detection moduleaccording to various embodiments described herein;

FIG. 14 illustrates yet another example of an electropherogramcharacteristic that will be detected by the peak detection moduleaccording to various embodiments described herein;

FIG. 15 illustrates yet another example of an electropherogramcharacteristic that will be detected by the peak detection moduleaccording to various embodiments described herein;

FIG. 16 illustrates yet another example of an electropherogramcharacteristic that will be detected by the peak detection moduleaccording to various embodiments described herein;

FIG. 17 illustrates an exemplary peak detection system according tovarious embodiments described herein;

FIG. 18 illustrates an example of a peak detection method according tovarious embodiments described herein;

FIG. 19 illustrates another example of a peak detection method accordingto various embodiments described herein;

FIG. 20 illustrates an exemplary progressive modulation filter accordingto various embodiments described herein;

FIG. 21 illustrates an example of a mapping peaks function according tovarious embodiments described herein;

FIG. 22 illustrates an example of a stutter characteristic according tovarious embodiments described herein;

FIG. 23 illustrates an example of a characteristic which may be mistakenfor stutter according to various embodiments described herein;

FIG. 24A-24E illustrates an example of stutter detection according tovarious embodiments described herein;

FIG. 25A-25E illustrates another example of stutter detection accordingto various embodiments described herein;

FIG. 26 illustrates a pure base square score assertion according tovarious embodiments described herein;

FIG. 27 illustrates a square score computation according to variousembodiments described herein;

FIG. 28 illustrates a mixed based square score assertion according tovarious embodiments described herein;

FIG. 29 illustrates a mixed base square score computation according tovarious embodiments described herein;

FIG. 30 illustrates an example of a square scores discriminationaccording to various embodiments described herein;

FIG. 31 illustrates an example of amplitude as a measure of confidenceaccording to various embodiments described herein;

FIG. 32 illustrates an example of amplitude score computation accordingto various embodiments described herein;

FIG. 33 illustrates an example of mixed-base ratio scoring according tovarious embodiments described herein;

FIG. 34 illustrates an example of amplitude score performance accordingto various embodiments described herein;

FIG. 35 illustrates an example of modulation as compared to amplitudeaccording to various embodiments described herein;

FIG. 36 illustrates an example of performance of modulation scoreaccording to various embodiments described herein;

FIG. 37 illustrates an example of variant scores according to variousembodiments described herein;

FIG. 38 illustrates an exemplary computing system for implementingvarious embodiments described herein; and

FIG. 39 illustrates an exemplary distributed network system according tovarious embodiments described herein.

DETAILED DESCRIPTION

To provide a more thorough understanding of the present invention, thefollowing description sets forth numerous specific details, such asspecific configurations, parameters, examples, and the like. It shouldbe recognized, however, that such description is not intended as alimitation on the scope of the present invention, but is intended toprovide a better description of the exemplary embodiments.

According to various embodiments of methods and systems describedherein, a number of innovative features to enable processing ofmixed-base sequence data produced from Sanger instrumentation, toproduce high-quality variant observations for subsequent investigationby researchers is provided.

FIG. 1 illustrates an exemplary workflow according to variousembodiments described by the present teachings. In the method of FIG. 1,more accurate variant calling in electropherograms is achieved byanalyzing and adjusting alignment, determining characteristics of theelectropherogram trace that could lead to error, and various scoringdeterminations. These functions are described in more detail below.

A Mechanism for Mixed-Base Sequence Analysis Support

Various embodiments of the present teachings described herein includethe following features, also illustrated in FIG. 2:

-   1.) Importation of sequence data in step 202.-   2.) Implementation of mixed-base support in high-performance,    off-the-shelf Stripped Smith-Waterman algorithm to produce    highly-accurate CIGAR string alignment representations in step 204.-   3.) Regeneration of CIGAR to capture mixed-base (heterozygous)    events in step 206.-   4.) Validation and qualification of mixed-base observations using    trace based analysis in step 208.-   5.) Generation of pure-base variant calls for incorporation in    standardized (VCF) output in step 210.    Implementation Mixed-Base Alignment Support    Query Sequence Import

According to various embodiments, in step 202, individual Sangersequences (reads) are imported into Query Sequence Records from FASTAformat and base call symbols are validated as indicating valid purebases or valid mixed-bases on the terms of membership in a BaseTranslation Table. The Base Translation Table is derived from thepublic-source table contained in a library, Stripped Smith-Watermanalignment algorithm described in PLOS (Zhao M, 2013). However, accordingto various embodiments, the table has been resized and populated toincorporate mixed-base calls as well as pure base calls. If invalid basesymbols are detected, the sequence is rejected and a warning is providedto the user. The FASTA header for the sequences is modified to supportadditional identifiers needed by the algorithms according to variousembodiments described herein. Additionally, the header includes theuntrimmed sequence length and the clear range definition. The processoremploying the algorithm according to various embodiments will comparethe length of the imported sequence to the length indicated by themodified FASTA formatted header. If a discrepancy exists, the read willbe rejected and a warning issued.

Sequence Orientation Detection

The method according to various embodiments implements an OrientationDetection function which identifies imported sequences as being forwardor reverse reading based on a preliminary alignment to the referencesequence. The Orientation Detection function is implemented using theNational Center for Biotechnology Information (NCBI) Basic LocalAlignment Search Tool (BLAST) algorithm, Megablast configuration. TheBLAST algorithm is retrieved from the NCBI C++ Toolkit which isavailable fromhttp://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_getcode_syn#ch_getcode_snv.ftp_download.According to various embodiments, the required modules from the NCBI C++Toolkit in the Orientation Detection function provide high-speed andhighly validated operation. The Orientation Detection Functiondetermines the sequence orientation based on the BLAST scores and theorientation detected by the BLAST algorithm. Should the score fail tomeet a criterion, the orientation of the sequence cannot be determinedand the Orientation Detection function will reject sample and notproduce an orientation record. The Orientation Detection functionrecords the orientation findings in a tab-delimited transfer file whichis used subsequence by the method of detecting variants. The file duringthe alignment processing is imported and validity of the file isdetermined. If a corruption in the format is detected, the alignmentprocess is aborted. Additionally, an imported sequence record for eachorientation record is checked.

An error will be provided if there is excessive orientation records orexcessive sequence records.

Sequence Reorientation

During sequence import, sequences identified as into the forward readingframe are converted. This is done by reversing the order of the bases inthe sequence and then obtaining the complement of the reversed bases byusing two mapping arrays and a high-speed linear search algorithm toidentify and translate the incoming base to its complement form,including mixed-base conversion.

Additional Sequence Validation

The sequences are further validated during import. The imported sequencelength is qualified and sequences whose length falls below a certainthreshold are rejected.

The ratio of the trimmed length is computed versus the untrimmed lengthof read and if the ratio falls below a threshold. Again, a warning willbe issued to indicate that the sample quality is suspect.

Additionally, the number of mixed-bases contained in the sequence iscounted. The ratio of mixed-bases to total sequence length is computed.

Should the ratio be excessive, a flag is set to imply further processingof the sequence. Any rejected sequences are maintained in a separatelist of failed samples for later reporting.

Reference Sequence Import

The reference sequence is imported into a Reference Sequence Record froma FASTA formatted input. The reference is assumed in the forward readingframe. The reference is validated to contain only pure bases. The lengthof the reference sequence is validated against the length indicated inthe modified FASTA header. Errors halt processing with a warning to theuser.

Alignment Database

An Alignment Database is created to save the sequence Alignment Recordsaccording to various embodiments described herein. These AlignmentRecords contain reference to the Query Sequence Record and the ReferenceSequence Reference as well as specific outcomes of the alignmentoperation. The database additionally is segregated to contain passingand failed Alignment Records.

Aligner Module

A module called Aligner is included in the method according to variousembodiments. The Aligner integrates the functionality of the StrippedSmith-Waterman (SSW) alignment algorithm identified with functions anddata storage schemes useful to facilitate mixed-base alignment forembodiments described herein.

Mixed-Base Alignment Configuration

The SSW alignment algorithm is parameter driven and comes with defaultsettings for pure-base alignment. Aligner defines additionalconfigurations of predefined constants used by the SSW algorithm tofacilitate mixed-based alignment in step 204, algorithm testing, andalgorithm validation. The default operational configuration supportsmixed-base alignment. In this mode the Aligner configures the SSWalgorithm to accommodate mixed-base symbols through configuring amodified Base Translation Table (described above), a mixed-base costmatrix (below) and gap opening, gap extension, mismatch penalties andmatch reward which our testing has revealed to produce contigs(consecutive stretches of alignments) which favor generation ofmismatches over gaps. Specifically, the SSW alignment algorithm willreward, rather than punish transitions between compatible bases. Inorder to determine compatibility of bases, the Aligner implements acompatible bases function. This function is optimized by firsttranslating the two involved base symbols from the evaluated sequences(reference and query) into a base index using the Base TranslationTable. Then using the indexes to determine the compatibility using theBase Compatibility Matrix, illustrated in FIG. 3.

For example, if an “A” is encountered in the reference and an “M” in thequery, which are compatible, the SSW alignment algorithm will mark thesebases as matching and will not open an alignment gap or impose amismatch penalty. Aligner execution uses the SSW algorithm to identifythe best fit between the reference and the query sequences and producesa Compact Idiosyncratic Gapped Alignment Report (CIGAR) string thatdescribes the differences between the reference sequence and the querysequence in an alphanumeric format. To facilitate high-speed processing,the Aligner converts the CIGAR string produced by the SSW algorithm intoa vector of CIGAR Operations, each of which is described as having alength and a type of: Match, Mismatch, Insert, and Deletion. The Alignerthe stores the CIGAR along with the beginning and ending positions ofthe aligned portion of the query sequence and reference sequence into anAlignment Record which it then records into the Alignment Database.

CIGAR Regeneration Module

Because the mixed-base alignment operation has treated compatiblemixed-bases as matches, and stored these in Match CIGAR Operations, theCIGAR Regeneration module is implemented in step 206 to identifycompatible mixed-bases in a regenerated CIGAR as Mismatches CIGAROperations. For each Alignment Record stored in the Alignment Databasethe CIGAR Regeneration module retrieves the CIGAR (Source CIGAR) and theQuery Sequence Record. The CIGAR Regeneration module additionallycreates a blank CIGAR (Target CIGAR) to hold the results of rewritingand also retrieve the relevant Query Sequence Record. For each Insert,Deletion, or Mismatch operation recorded in the Source CIGAR, the CIGARRegeneration module creates an identical operation and inserts it intothe Target CIGAR. For each Match operation in the Source CIGAR, theCIGAR Regeneration module examines the bases in the corresponding regionof the Query Sequence Record to identify pure-bases and mixed-bases(described previously). The CIGAR Regeneration module aggregates thepure bases into a Match operation. If a mixed-base is encountered, theCIGAR Regeneration module terminates and emits any current Matchoperation, initiates a Mismatch operation, and aggregates allconsecutive mixed-bases into the Mismatch operation. If a pure baseshould subsequently be encountered or if the end of the Match operationin the Source CIGAR is encountered, the CIGAR Regeneration module willemit the mismatch operation. When all the CIGAR Operations contained inthe Source CIGAR have been processed and the matching (compatible)mixed-bases have been processed into Mismatch operations in the TargetCIGAR, the CIGAR Regeneration module replaces the Source CIGAR with theTarget CIGAR in the Alignment Database and proceeds to the nextAlignment Record until all Alignment Records have been processed.

Alignment Score Calculation

The CIGAR Regeneration module provides an efficient opportunity tomeasure the quality of the resulting alignment of the query sequence andthe reference sequence. During generation of the Target CIGAR, the CIGARRegeneration module maintains counts of the number of matching bases,mismatching bases, inserted bases, and deleted bases. The CIGARRegeneration module computes an alignment score as follows:

${{Aero}\mspace{14mu}{Alignment}\mspace{14mu}{Score}} = {\left( \frac{Matches}{{Matches} + {Mismatches} + \mspace{40mu}{Inserts} + {Deletions}} \right)*100.0}$

While there is great diversity in alignment scoring, testing revealsthat the Alignment Score provides good discrimination between wellmatching sequences and poorly matching sequences which are typicallyanticipated to be submitted to the system. Specifically, this scoreincorporates the balance of insertions and deletions with equal balanceto lend a metric of overall comparability.

Alignment Score Filter

Alignment Records may have a low Alignment Score because of poor samplequality, large areas of genomic variability, or because an inappropriatereference sequence has been specified. An Alignment Filter module isimplemented to identify Alignment Records whose Alignment Score fails topass a user specified Alignment Score Cutoff. In these failing cases,the Alignment Filter module transfers the Alignment Record from thepassing section in the Alignment Database to the failed section in thealignment database, and issue an appropriate warning. Users can thenre-run their analysis with a lowered Alignment Score Cutoff if they feelthis classification is inappropriate for their research.

Storage of Alignment Results

Alignment Records marked contained in the Good segment of the AlignmentDatabase are ready for mixed-base variant analysis.

A Mechanism of Signal Processing in Sanger Base Sequencing

1 The Solution

Various embodiments described herein improves on the results of knownalgorithms that interpret electropherograms, and includes high-qualityprocesses to accommodate many of the conditions identified above. Alimitation of the previously-used algorithms is that it is “other sampleagnostic.” That is it is unable to take advantage of informationincluded in other sequences. The embodiments described herein can fillthis gap, first by providing a second order correction atop previousalgorithms and also by using information from samples the user hasgrouped together to improve detection and accuracy.

The goal of the Trace Analysis module is to convert luminescent signalsinto biological signals, and to capture sufficient metrics to supportscoring and validation which is shown in FIG. 4.

Reference Frames

The base call sequences are referenced in a number of different waysthroughout the application. The reference frames depicted in FIG. 5 aredefined by various embodiments described herein.

2 Trace Analysis Implementation

To prepare for Trace Analysis, the Electropherogram data is imported instep 402. The electropherogram data is received from the algorithmpipeline in a FASTA format but with proprietary formatted headers thatindicate the contained data type. The Analyzed Trace Data is importedfrom the Electropherogram data for each of the four electropherogramchannels. It additionally extracts the Peak Location data, theidentification of the electropherogram sample from which the KB Callerproduced the primary and secondary base call. Each channel of theAnalyzed Trace Data is verified as well as the Peak Location data arepresent for each imported Query Sequence Record and that their length isconsisted with the corresponding query sequence. Samples are rejectedfrom further processing if they fail this validation.

The passing samples are added into the Query Sequence Database forsubsequent access.

Next, the Alignment Database is accessed and each Alignment Record isreviewed to process its corresponding CIGAR. Each Insert, Deletion, andMismatch CIGAR Operation is converted into a variant candidate describedin a Variant Record. In cases where the CIGAR Operation indicates alength which is greater than 1 base pair, multiple Variant Records areproduced for each base. The Variant Record describes the variant event,i.e. mismatch, insert, or deletion, includes the location of the variantin the reference sequence, and also in the query sequence. A variantstring is additionally produced which indicates the bases involved inthe variant, for example the fact that “A is substituted with T” wouldbe captured. References to the Query Sequence Record, the ReferenceSequence Record, as well as the Alignment Record are saved. These(candidate) Variant Records formulate the basis for subsequent TraceAnalysis.

2.1 Trace Analysis Initialization

Another feature according to various embodiments is execution of traceanalysis in the mixed base variant validation/qualification of step 208of FIG. 2. Trace analysis is initialized in step 404. Eliminating thisnon-productive analysis saves significant computation resources andprovides near real-time results to the end-user. To accomplish this, asillustrated in Error! Reference source not found. 6, a region 600 in theforward reading query reference frame surrounding the point of interestis identified; that is, the base call position giving rise to theobservation of mismatch or insertion, or the two base call positionsgiving rise to the observation of a deletion variant. To provide astatistical basis for certain calculations, the trace analysis isextended by two additional base call positions preceding and followingthe point of interest. Because the trace analysis begins with thedetection of a valley of a peak, an additional base call position isadded to both ends to define the region of the trace on the traceanalysis is performed. Positioning either before the beginning of theelectropherogram or exceeding beyond the end is avoided. To access datafrom the electropherogram, the range in the forward reading queryreference frame is mapped to the original called-based reference frame,which depends on the original orientation of the sequence data alongwith the clear range locations. The called-base frame is then convertedinto the electropherogram reading frame with assistance of the TraceCall Positions (PLOC). FIG. 7 provides additional detail to thisprocess. Analysis of a statistical number of electropherogram traces inthe development of various embodiments described herein have assisted usin fine tuning the computation of these ranges to provide high accuracyand consistent results in defining consistent region for trace analysis.

2.2 Peak Detection

The goal of the Peak Detection module in step 406 of FIG. 4 is toconvert the sequence of electropherogram data points into a discretecollection of signal observations (peaks.) A goal is to capture everymeaningful inflection of the electropherogram with only cursory concernto validating the observations in the continuous form. Subsequent TraceProcessing validates the signal observations as well as the biologicalsignificance, and we have only a cursory concern to validate theobservations during the peak detection from the continuous form.

The detection of peaks is complicated due to an irregular nature of theelectropherogram peaks. As illustrated in FIG. 8, in a high-qualityelectropherogram, most peaks have a Gaussian shape with modulation thatclearly rises above the noise floor and with little interference betweenthe peaks. Note that the peaks are very evenly spaced and of nearlyidentical width. In this example, it is also likely that each peak has asingle point of inflection where the height transitions from rising tofalling, a single peak. In this case, the Peak Detection module willaccurately detect and produce a sequence of peak objects. Each peakobject describes the peaks apparent on the electropherogram, includingthe position, the width, the height the modulation, and sequence ofthese peaks.

As illustrated in FIG. 9, electropherograms can also report mixed-basesequences. In this high-quality example, the two base modules are ofnearly identical size and amplitude. There is no evident noise, and theyare perfectly aligned. In this near perfect mixed-base example, the PeakDetection module of step 406 produces a list of peaks, including a peakfor each of the green as well as black overlapping peaks (6 peaks intotal for the example shown below.)

FIG. 10 illustrates a case where the Peak Detection module routinelyaccommodates peaks which have a flattened portion, or a very nearly flatregion on top, resulting in a clean inflection on its left and rightside with no significant inflection between. Because of thehigh-precision required for the system, the Peak Detection module mustreport these peaks in a precise fashion.

FIG. 11 provides an example of a signal (1102) which is biased highabove the noise threshold but which has very low modulation. If thesepeaks were on the noise floor, they would compete unfavorably withnoise. However, as biased to a high amplitude, these low-modulationpeaks are generally valid biological signals. The Peak Detection moduleof step 406 will detect and produce peak objects in this case.

FIG. 12 illustrates the region 1202 that signal quality is typically lowat the ends of the electropherogram. The peaks become diffuse and mixed.Typically this data is removed in quality trimming prior to processing.However, in some cases residual low-quality bases will remain. This is awell characterized phenomena. In this case, the Peak Detection module ofstep 406 may produce many peaks based on the various tuning parameters.Some of these peaks may represent valid biological signals while somepeaks may represent signal noise and be subsequently rejected.

FIG. 13 depicts another phenomena that exists is shoulder-peaks inregion 1302, in which two peaks are characterized by the first rising toa plateau, but not descending in a valley, and followed immediately by arise to a taller peak. The same kind of shoulder-peak can occur on thefalling size, when a tall peak descends to a plateau followed by adescent to the noise floor. In this case the Peak Detection moduledetects the shoulder peak condition and produce two peaks. Parametersdetermine the limits for this detection.

Error! Reference source not found. 14 shows an example of an extendedvalley with a slowly rising, low slope which interferes with twoproceeding peaks before rising to a legitimate peak itself in trace1402. This slope, which begins in the noise region, rises to the levelof a mixed base and could inadvertently trigger a false mixed-base callby KB caller.

Error! Reference source not found. 15 provides an example of a cleanelectropherogram with a glitch resulting in two exaggerated peaks (inregion 1502). An additional elongated peak (green) lies below those two.These irregularities are sometimes referred to as dye blobs. The truepositive inflection is preserved in these but not produce false positivecalls.

FIG. 16 shows a case similar to that above, but having an irregularelongated peak (1602). This peak spans three well-formed peaks andresults in KB Caller producing two mixed base calls. The Peak Detectionmodule should detect this peak, but enable its subsequent removal.

The Peak Detection module processes each Variant Record from the VariantRecord Database to detect peaks, which represent detection of aparticular DNA base in a specific relative sequence from the sampledelectropherogram data. Subsequent processing during Trace Analysisperforms additional validation of these peaks, and they undergosignificant subsequent process before they are declared valid biologicalobservations of variance to the reference sequence.

FIG. 17 provides an overview of the data organization which supports thePeak Detection module. For each Variant Record (variant candidate), thePeak Detection module processes the electropherogram data associatedwith the variant candidate's Query Record. Each of the four channels(Analyzed Trace Data) is processed independently, considering each datapoint through the region of the electropherogram identified during TraceAnalysis Initialization, described above. During processing the PeakDetection module produces Peak Records and adds these into a PeakCollection database that is associated with the considered VariantRecord. The Peak Detection module populates the Peak Record with thefollowing basic information: trace channel on which the peak wasidentified, corresponding to the DNA bases of G, A, T, and C, LeftValley position and height, Peak position and height, and Right Valleyposition and height.

The Peak Detection module characterizes a peak as having a left andright valley and a peak. The Peak Detection module implements a statemachine to facilitate detection with the transitions: Seeking LeftValley, Seeking Left Peak, Seeking Right Peak, and Seeking Right Valley.

FIG. 18 illustrates the detection of non-shoulder peaks.

-   1.) Upon the initial entry into each channel, the Peak Detection    module initializes various state variables in order to avoid an    initial state transition when processing the first trace point. The    Peak Detection Module sets the machine into the Seeking Left Valley    state.-   2.) The Peak Detection module will sequentially consider analyzed    data points and calculate the slope as the difference of the current    and last data point's height. It will not change the state of the    machine from Seeking Left Valley state so long as the slope remains    moderate and neither steeply positive or steeply negative.-   3.) If the Peak Detection module encounters a steep positive slope    it will set the machine into the Seeking Left Peak state, and    remember the position and height of the last considered data point    as the Left Valley position and height.-   4.) The Peak Detection module will remain in the Seeking Left Peak    state while considering data points remain steeply positive.-   5.) If the Peak Detection module encounters a reduction of the slope    from steeply positive to moderately positive, but more positive than    steeply negative, then the Peak Detection module will set the    machine to the Seeking Right Peak state and remember the Left Peak    height and position as the taller of the current or last data    point's height and position.-   6.) If instead the Peak Detection module encounters a steeply    negative slope, it will set the machine into the Seeking Right    Valley state and remember the Left Peak height and position as well    as the Right Peak height and position as the taller of the current    or previous data point's height and position.-   7.) The Peak Detection module remains in the Seeking Right Peak    state while the slope of the considered data points is more positive    than steeply negative.-   8.) If the Peak Detection module encounters a transition of the    slope to steeply negative, then the Peak Detection module will set    the Seeking Right Valley state and store the Right Peak height and    position as the taller of the current or last data point's height    and position.-   9.) The Peak Detection module remains in the Seeking Right Valley    state while the slope of the considered data points is steeply    negative.-   10.) If the Peak Detection module encounters a moderate slope more    positive than steeply negative and not as positive as steeply    positive, then the Peak Detection module will set the machine to the    Seeking Right Valley state and remember the Right Valley height and    position as the current data point's height and position. The Peak    Detection module will proceed to create a Peak Record with the    remembered Left Valley height and position, the Peak height and    position, being the average of the Left Peak height and position and    the Right Peak height and position, and with the Right Valley height    and position. The Peak Detection module will add the new Peak Record    to the Peak Record Database, associated with the variant candidate    under consideration.-   11.) If instead, the Peak Detection module encounters a steeply    positive slope, then the Peak Detection module will set the machine    to the Seeking Left Peak state and remember the Right Valley height    and position as the current data point's height and position. The    Peak Detection module proceeds to create a Peak Record and add it to    the Peak Record Database as previously described. Additionally, the    Peak Detection module sets the Left Valley height and position to    the Right Valley's height and position.

The Peak Detection module continues to process data points for the fourtraces, compiling Peak Records into the Peak Record Database until therange described during Trace Analysis Initialization (Section TraceAnalysis Initialization2.1) is consumed.

The Peak Detection module additionally implements detection for shoulderpeaks as illustrated in FIG. 13. Shoulder peaks “add-on” to a currentlybuilding peak without having a descent to a valley. FIG. 19 illustratesthe state machine diagram for detection of shoulder peaks.

-   -   1.) While the machine is in the Seeking Left Valley state, the        Peak Detection module sequentially considers analyzed data        points and calculate the slope as the difference of the current        and last data points' heights. It will not change the state of        the machine from Seeking Left Valley state so long as the slope        remains moderate and is neither steeply positive nor steeply        negative.    -   2.) If the Peak Detection module encounters a steep negative        slope, the distance from the last peak position and also the        height of the current declining data point are evaluated. If the        distance from the last peak is below a minimum, or the current        data point's height is too low, the Peak Detection module leaves        the machine in the Seeking Left Valley state.    -   3.) Otherwise, the Peak Detection module computes the Left        Valley position as the greater of the last Right Valley position        and the current position less the minimum detection distant. The        Left Valley height is computed from the actual trace height at        the computed Left Valley Position. The Left Peak height and        position and the Right Peak is stored as the current position.        Finally, the Peak Detection module sets the machine to the        Seeking Right Valley state.    -   4.) While the machine is in the Seeking Right Peak state, the        Peak Detection module sequentially considers analyzed data        points and calculates the slope as the difference of the current        and last data points' heights. The state of the machine from        Seeking Right Peak state does not change so long as the slope        remains moderate and is neither steeply positive nor steeply        negative.    -   5.) If the Peak Detection module encounters a steep positive        slope, the distance from the last Left Peak position and also        the height of the current data point are evaluated. If the        distance from the last Left Peak is below a minimum, or the        current data point's height is too low, the Peak Detection        module leaves the machine in the Seeking Right Peak state.    -   6.) Otherwise, the Peak Detection module stores the Right Peak        height and position as equal to the Left Peak height and        position, and stores the Right Valley position as the current        data point's position and the Right Valley height as the lower        of the Right Peak's height and the current data point's height.        The Peak Detection module creates a new Peak Record based on the        Left Valley, the Peak, and the Right Valley and adds it to the        Peak Record Database. A new peak is stored by storing the Left        Valley position as the greater of the Right Valley position and        the current position less the minimum detection distance.        Finally the Peak Detection module sets the machine to the Seek        Left Peak state.        2.3 Peak Pruning

The purpose of peak pruning (step 408 in FIG. 4) is to eliminate signalobservations (peaks) which fail validation certain metrics. This processprovides a first-pass filter on the interpretation of the continuousdata into discrete observations on common signal properties. The PeakPruning Module considers all the peaks produced by the Peak Detectionmodule as follows:

2.3.1 Amplitude Filter

The Peak Pruning module applies a minimum height filter to all peaks.Peaks whose height falls below the minimum level are marked for deletionand receive no further consideration. The threshold for this filter isdetermined by analyzing a large set of expertly curated data whichincluded broad diversity regarding experimental design, instrumentation,and data quality. According to various embodiments, a threshold isselected so that no legitimate signal is excluded but rather thatsignals may be distinguished from background noise.

2.3.2 Progressive Modulation Filter

To distinguish signals from noise, a filter is imposed on the degree ofmodulation for a peak to be considered a valid signal. Error! Referencesource not found. 11 illustrates a phenomena which is encountered wherea bias boosts the height of a signal peak and also the signal valley.The signal, if occurring on the signal floor would have insufficientmodulation to rise above the noise. However, at the higher amplitudethere is no competition for the noise and the modulation stringency canbe relaxed. The Peak Pruning module applies a progressive modulationfilter which is tuned so that signals require greater modulation whenthey have low amplitude and less modulation when they have greateramplitude.

Error! Reference source not found. 20 describes the design of theprogressive modulation filter. The peak height determines the modulationcutoff; that is the modulation below which the peak will be rejected.

The signal modulation module is designed to normalize non Gaussianpeaks, to eliminate the effect of long leading and trailing tails, andto provide a degree of algorithmic normalization to shoulder peaks. Themodulation is computed as follows:

-   1.) For the computation of modulation, the peak is considered as a    left-side right triangle and a right-side right triangle.-   2.) The effective left-side valley position is the larger of the    detected left-side valley position and the peak position, less the    nominal half-peak width.-   3.) The effective right-side valley position is the smaller of the    detected right-side valley position and the peak position plus the    nominal half-peak width.-   4.) The effective left-side valley height is the actual trace height    at the left-side valley position. The effective left-side valley    height is further limited to the height of the peak height.-   5.) The effective right-side valley height is the actual trace    height at the right-side valley position. The effective right-side    valley height is further limited to the height of the peak height.-   6.) The effective valley height is the less of the effective    left-side valley height and the effective right-side valley height.-   7.) The modulation is the peak heights less the effective valley    height.    In application of the progressive modulation filters:-   1.) The height of the peak is computed and compared to the    progressive modulation definition (Error! Reference source not    found. 20).-   2.) If the height of the peak exceeds the peak modulation ceiling,    the peak is considered to have passed the peak modulation filter.-   3.) Otherwise, if the height of the peak falls below the minimum    peak modulation height, the peak is considered to have failed the    peak modulation filter.-   4.) Otherwise, the modulation of the peak is computed as described    above.-   5.) A modulation score is computed as the ration of the peak    modulation and the Min Peak Modulation as described above.-   6.) For cases where the ratio is greater than one, the peak is    considered as passing the progressive peak modulation filter. In    cases where the ratio is less than one the peak is considered to    have failed the peak modulation filter, however the peak is not    marked for deletion, but is rather assigned a Low Modulation flag is    set on the peak and the modulation score is recorded for subsequent    consideration during variant scoring.    2.3.3 Minimum Peak Width Filter

Peaks which are detected with abnormally narrow width do not conveybiological information and will receive no further consideration. ThePrune Peak module:

-   -   1.) Compute the width of the peak as the detected right valley        position less the detected left valley position.    -   2.) If the width falls below the minimum width threshold, the        peak is marked for deletion        2.3.4 Excessive Peak Width Filter

Peaks may be detected with excessive width do not convey biologicalinformation and will receive no further considerations. The Prune Peakmodule:

-   -   1.) Compute the width of the peak as described above.    -   2.) If the width exceeds a maximum width threshold, the peak is        marked for deletion.        2.4 Intersection Detection and Calculation

With reference back to FIG. 4, the Intersection Detection andCalculation module in step 410 identifies the intersection, or overlap,of adjacent peaks. The computation of intersection is critical indetection of mixed-base peaks and also of interference. Further, theintersection is used as a critical factor in determining variantdiscrimination and confidence scoring. This process is uniquelyimplemented in the methods and systems described herein to beefficiently executed and produce highly accurate and unbiased results.The computation of intersection consists of two modules, detection ofintersection and computation of the intersection. The detection ofintersections is performed in an optimized fashion, using two indexeswhich slide through the data points to minimizes the total number ofcomputations involved. The computation of intersection follows detectionand is performed based on the detected intersections. Because peaks maybe asymmetric, particularly in the case of shoulder peaks, the valleysof the primary and each subordinate peak are normalized in a fashion toprovide the fairest numeric benefit to asymmetric peaks prior tocomputation of intersection. Additionally, to normalize comparisons ofpeaks resting on the noise floor to those which have an amplitude bias,the computation of intersection only considers the modulated portion ofthe trace. Finally, irregularities can occur such as the subordinatebeing larger than the primary peak, or traces dipping below thenormalized valley are addressed to prevent inaccurate computation ofintersection.

2.4.1 Intersection Detection

The Intersection Detection and Calculation module detects intersectionsbetween peaks as follows:

-   1.) The Intersection Detection and Calculation module is invoked to    consider the Peak Database for each Variant Record in turn.-   2.) For each Peak Database, the Intersection Detection module orders    the peaks in order of ascending Left Valley position.-   3.) The Intersection Detection and Calculation module maintains two    indexes, one for the primary peak and one for secondary peaks. The    primary peak is the peak for which intersections are being    identified. The secondary peaks are the peaks which are being    evaluated for intersection.-   4.) The Intersection Detection and Calculation module checks to    determine if the Right Valley of the secondary intersects with the    Left Valley of the Primary, and if the overlap is greater than the    minimum overlap, then a reference to the secondary peak is added as    a subordinate in the primary Peak Record.-   5.) The Intersection Detection and Calculation module checks to    determine if the Left Valley of the secondary intersects with the    Right Valley of the Primary, and if the overlap is greater than the    minimum overlap, then a reference to the secondary peak is added as    a subordinate in the primary Peak Record.-   6.) The Intersection Detection and Calculation module remembers the    last productive position of the secondary index and updates it when    the secondary peak falls fully behind the primary peak in order to    avoid performance of unnecessary comparisons or to miss potential    intersections.    2.4.2 Intersection Calculation

The computation of intersection follows the detection and is computed asfollows:

-   1.) For the computation of the intersection, compute the primary    peak's effective valley height:    Effective Left Valley Position=max(Detected Left Valley    Position,Detected Peak Position−Half Peak Width Constant)    Effective Right Valley Position=min(Detected Right Valley    Position,Detected Peak Position+HalfPeak Width Constant)    Effective Left Valley Height =min(Trace Height[Effective Left Valley    Position],Detected Peak Height)    Effective Right Valley Height =min(Trace Height[Effective Right    Valley Position],Detected Peak Height)    Effective Valley Height=min(Effective Left Valley Height,Effective    Right Valley Height)-   2.) For every trace data point (Trace Height) between the Effective    Left Valley Position and the Effective Right Valley Position. For    each point compute:    Effective Primary Height[i]=max(0,Primary Trace Height[i]−Effective    Valley Height)-   3.) Compute the primary peak's area:    Primary Peak Area=ΣEffective Primary Height[i]-   4.) For every trace data point between the Effective Left Valley    Position and the Effective Right Valley Position (j), and for each    subordinate peak (i), compute:    Effective Subordinate Height[i,j]=min(max(0,Subordinate Trace    Height[i,ji]−Effective Valley Height),Effective Primary Height[i])-   5.) For every trace data point between the Effective Left Valley    Position and the Effective Right Valley Position (j), and for each    subordinate peak (i), compute:    Subordinate Intersection[i,j]=min(Effective Subordinate    Height[i,j],Effective Primary Height[j])-   6.) For every trace data point between the Effective Left Valley    Position and the Effective Right Valley Position (j), compute:    Largest Subordinate Intersection[j]=max(Subordinate    Intersection[0],Subordinate Intersection[1] . . . Subordinate    Intersection[n])-   7.) Compute the overlap area as:

${{Overlap}\mspace{14mu}{Area}} = {\underset{\mspace{14mu}{{{Effective}\mspace{14mu}{Left}}\mspace{14mu}{{Valley}\mspace{14mu}{Position}}}}{\sum\limits^{\mspace{11mu}{{{Effective}\mspace{14mu}{Right}}\;{{Valley}\mspace{14mu}{Position}}}}}{{Largest}\mspace{14mu}{Subordinate}\mspace{14mu}{{Intersection}\lbrack f\rbrack}}}$2.5 Map Peaks

The purpose of the Map Peaks module in step 412 of FIG. 4 is to alignpeak observations with the base call produced by KB Caller. Mapping thetrace analysis observations with the KB Caller results is criticalbecause the KB Caller produces the basic hypothesis for variants, andthe trace analysis reinforces or refutes that hypothesis. Incorrectmapping will generally result in reinforcing an invalid base call orrefuting a valid base call. With high-quality traces that have regularwell-formed peaks, a trivial implementation might adequate, however theanalysis of traces which have a high level of a repeated bases, or withhighly degraded signals in the trace ends, there is a significantopportunity to encounter peaks which are out of cadence, and alsomultiple peaks that compete for the same base call position. A worstcase occurs when a peak falls equally between two base call positions.Analysis of a large highly curated data set has revealed that thespacing between peaks is regular within a certain range of values, andthis knowledge is used in the mechanization of the mapping functiondescribed below.

The mapping of peaks to base call query position is performed asfollows, and is illustrated in FIG. 21:

-   -   1.) Order the peaks in ascending order based on the Left Valley        position.    -   2.) For each Peak, consider each Query Position in the query        range defined during Trace Analysis Initialization (Section        2.1), from first to last.    -   3.) Convert the Query Position from the Forward Reading        reference frame into an index in Base Call coordinates for        forward reading samples as follows:        Base Call Index=Query Position+Clear Range Start Position    -    and for reverse reading samples        Base Call Index=Query Length−1−Query Position+Clear Range Start        Position    -   4.) Obtain the Trace Coordinate for the considered query        position from the Trace Call Position (PLOC) using the Base Call        Index.    -   5.) Compute the Mapping Distance as the difference between the        Trace Coordinate identified from the Query Position and the Peak        Position determined during Peak Detection (Section 2.2).    -   6.) Iterate over the Query Range until the distance has reached        a minimum and begins to grow larger. Retain the query identifier        for the smallest distance.    -   7.) If the distance is within a maximum mapping window limit,        set the Query Position into the peak.    -   8.) If a peak maps equally to two base calling positions, it is        ambiguous. Issue a warning that the Peak cannot be mapped to a        base call.    -   9.) Finally, all the unmapped peaks are deleted.        2.6 Stutter Processing

The purpose of the Stutter Processing module of step 414 in FIG. 4 is toeliminate signal noise which might give rise to false positive outcomesotherwise. Stutter is a well-known phenomenon associated with Sangersequencing. It seems to frequently begin with homopolymorphic region andthen can continue throughout the trace or come to an end. It cangenerally be easily recognized by manual inspection, but it has beendifficult to detect and remove with a high degree of accuracy throughautomated processing.

FIG. 22 provides a good example of stutter. Note the mixed base calls(2202.) Examination of the trace shows that these occur each time thereis a legitimate tall peak preceded by a diminutive peak, the stutterpeak, which falls beneath another legitimate peak.

FIG. 23 shows an example of a trace which has many characteristics ofstutter, but is not.

We are careful about eliminating stutter peaks because not every mixedbase results from stutter and not every time a small peak follows a tallpeak is that invalid. The approach, according to various embodiments, isto apply a set of rules to the trace region that generally characterizestutter to produce a stutter score, then if the score is high enough,the stutter module of the peak is removed.

We have developed a unique set of rules which we apply to trace regionsaround a mixed base variant to determine if stutter removal should beapplied. These rules are:

-   -   1.) Stutter detection is only applied to traces which have a        high mixed-base rate. This is because incidental mixed bases are        almost never stutter, and traces with stutter phenomena        typically have a marked increase in the mixed-base rate.    -   2.) Incidental observations of stutter are not absolute, however        review of a trace region around the point of interest can        discriminate stutter. This happens in part because the traces        around a stutter region are frequently “busy” already and so        sometimes detection can be confused. Also, the tuning of        detection filters, to operate over a wide range and variation of        traces sacrifices some determination.    -   3.) Stutter peaks are characterized by a taller peak followed        by, or proceeded by a diminutive peak which is always below        another peak. The diminutive peak is the stutter peak, and it        should not enter into analysis.    -   4.) The stutter peak may proceed or follow the primary peak, and        the pattern of leading or following will remain set throughout        an entire stutter region, however determination of this in a        short trace region is not possible due to phasing effects.        However, determining stutter using a “both ways” stutter        detection will resolve issues regarding directionality.    -   5.) The heights of the primary peaks and stutter peaks can be        separated and used as a filter. Our analysis has revealed a        range of heights between which stutter can be discriminated from        simple noise, for example, and also from clear subsequent        signals.    -   6.) The ratio of the primary and stutter peak can be further        used to discriminate stutter from legitimate signals. To apply a        sharp deadband on heights, we must also specify a ratio into        which stutter peaks must fall. For example, two peaks which are        nearly the same height cannot be stutter.    -   7.) Stutter peaks which are too low should be ignored. These        will also be below the detection limit required to generate or        support a call.    -   8.) For stutter detection, it is desirable for sensitivity to        check trace height rather than require a peak detection. The        stutter peaks may not be detected as peaks, but still can        support a general detection of stutter.    -   9.) It is desirable to detect stutter in a trace region, even if        it lends no specific identification of a stutter peak because        the calls in a stutter region are less reliable than those in a        clean region. We tag peaks differently if they are detected as a        stutter peak or if they are in a region of stutter presence for        use in scoring.        2.6.1 Stutter Processing    -   1.) Consider the ratio of the count of mixed-base occurrences        called by KB Caller and the count of all the bases.    -   2.) If the ratio exceeds a threshold, subject the trace to        stutter processing, otherwise do not process it for stutter.    -   3.) Sort the peaks based on the query position    -   4.) Calculate the stutter rate    -   5.) Compute a stutter score from the stutter rate    -   6.) Apply this stutter score to all the peaks in the Peak Record        Database    -   7.) If the peak is not a stutter peak, set a flag to mark it as        Associated with Stutter.        2.6.2 Stutter Rate Calculation    -   1.) Compute the NP1 stutter counts and also the number of peaks        processed.    -   2.) Compute the NM1 stutter counts and also the number of peaks        processed.    -   3.) Convert these counts into an NP1 and a NM1 rate.    -   4.) Compute a summarized stutter rate as the sum of both rates,        limited to 1.0        2.6.3 Compute NP1 Stutter        FIGS. 24A-24E are described as follows:    -   1.) Process every peak in the Peak Record Database as the        Primary Peak in step 2402.    -   2.) If the Primary Peak's Query Position has not been mapped,        proceed to the next Primary Peak.    -   3.) Obtain the Primary Peak's Query Position.    -   4.) Increment the number of NP1 Peaks Processed.    -   5.) Increment the Primary Peak's Query Position to produce a        Next Peak Query Position.    -   6.) Access the Peak Record Database to obtain the Next Peak        using the Next Peak Query Position. If the Next Peak cannot be        obtained, proceed to the next Primary Peak.    -   7.) Determine the trace channel (DNA base) of the Primary Peak.    -   8.) Find the tallest trace, other than the Primary Peak's trace        channel, at the Next Peak Query Position.    -   9.) Find the height of the Primary Peak's trace channel at the        Next Peak Query Position. This is the Compatible Trace.    -   10.) If the Compatible Trace's height is below the Minimum Trace        Height value, then it cannot be considered for a stutter peak        and proceed to the next Primary Peak.    -   11.) If the Compatible Trace is not below another trace, then it        cannot be considered as a stutter peak and proceed to the next        Primary Peak.    -   12.) If the Primary Peak's height is below a minimum level, then        it cannot be considered as a stutter peak and proceed to the        next Primary Peak.    -   13.) If the Compatible Trace's height is below a Minimum Trace        Height Level then it cannot be considered as a stutter peak and        proceed to the next Primary Peak.    -   14.) Determine the ratio of the height of the Compatible Trace        to the Primary Peak. If the ratio is greater than a Maximum        Stutter Peak Ratio, then is cannot be considered as a stutter        peak and proceed to the next Primary Peak.    -   15.) The findings are consistent with stutter detection.        Increment the NP1 Stutter Count.    -   16.) If the Next Peak has the same trace channel as the Primary        Peak Trace Channel, then mark it as “Stutter Detected”,        otherwise search through the Peak Record Database for a peak        with the same trace channel as the Primary Peak Trace Channel        and with a Query Position of the Next Query Position. If found,        mark that peak as “Stutter Detected.”    -   17.) Proceed to the next Primary Peak.        2.6.4 Compute NM1 Stutter        FIGS. 25A-D are described as follows:    -   1.) Process every peak in the Peak Record Database as the Prior        Peak.    -   2.) If the Prior Peak's Query Position has not been mapped,        proceed to the next Prior Peak.    -   3.) Obtain the Prior Peak's Query Position.    -   4.) Increment the number of NM1 Peaks Processed.    -   5.) Increment the Prior Peak's Query Position to produce a        Primary Peak Query Position.    -   6.) Access the Peak Record Database to obtain the Primary Peak        using the Primary Peak Query Position. If the Primary Peak        cannot be obtained, proceed to the next Prior Peak.    -   7.) Determine the trace channel (DNA base) of the Primary Peak.    -   8.) Find the tallest trace, other than the Primary Peak's trace        channel, at the Prior Peak Query Position.    -   9.) Find the height of the Primary Peak's trace channel at the        Prior Peak Query Position. This is the Compatible Trace.    -   10.) If the Compatible Trace's height is below the Minimum Trace        Height value, then it cannot be considered for a stutter peak        and proceed to the next Prior Peak.    -   11.) If the Compatible Trace is not below another trace, then it        cannot be considered as a stutter peak and proceed to the next        Prior Peak.    -   12.) If the Prior Peak's height is below a minimum level, then        it cannot be considered as a stutter peak and proceed to the        next Prior Peak.    -   13.) If the Compatible Trace's height is below a Minimum Trace        Height Level then it cannot be considered as a stutter peak and        proceed to the next Prior Peak.    -   14.) Determine the ratio of the height of the Compatible Trace        to the Primary Peak. If the ratio is greater than a Maximum        Stutter Peak Ratio, then is cannot be considered as a stutter        peak and proceed to the next Prior Peak.    -   15.) The findings are consistent with stutter detection.        Increment the NM1 Stutter Count.    -   16.) If the Prior Peak has the same trace channel as the Primary        Peak Trace Channel, then mark it as “Stutter Detected”,        otherwise search through the Peak Record Database for a peak        with the same trace channel as the Primary Peak Trace Channel        and with a Query Position of the Prior Query Position. If found,        mark that peak as “Stutter Detected.”    -   17.) Proceed to the next Prior Peak.        2.7 Merge Peaks

The purpose of the Merge Peaks function in step 416 of FIG. 4 is tocombine independent pure-base signals into mixed-base detections. Mixedbases can occur when we have detected two peaks that map onto the samequery position.

2.7.1 Identify Merge Candidates

-   -   1.) Sort the peaks in ascending query position.    -   2.) Traverse the peaks from first to last query position        considering each in turn.    -   3.) Obtain the peak's query position. Skip any unmapped peaks.    -   4.) If this is the first peak, then add the peak to the merge        candidates list.    -   5.) Otherwise, if this peak's query position matches the last        peak's query position then added to the merge candidates list        and process the merge candidate list as described in section        2.7.1 and empty it.    -   6.) Add the considered peak into the merge candidate list.    -   7.) Continue until all the peaks have been considered and        processed.        2.7.2 Process Merge Candidates

The goal of this module is to create a final list of base calls forsubsequent interpretation and for variant scoring. Specifically, thismodule merges multiple peaks mapping to the same query position into asingle peak. It attempts to make the best choices with a bias toreproduce the base call produced by KB Caller. The reason for this isnot to slovenly reproduce KB results, but to rather assemble the sametrace configuration that KB used in order to produce the variant score.In cases where it is not possible to reproduce the KB configuration ofbases, the best peaks are selected, the most highly modulated, as thebase candidate. The following steps describe this process.

-   -   1.) Obtain the query position for the items in the merge        candidates list.    -   2.) Obtain the base call produced by KB Caller for that query        position.    -   3.) If the KB Caller called base is a pure base, then        -   a. Select the candidate from the merge candidate list which            matches the KB called base and add it to the merged bases            list.        -   b. If no matching base can be found, select the candidate            which has the greatest modulation from the merged peaks            list.    -   4.) If the KB Caller called a mixed base        -   a. Hunt through the merge candidates list in an attempt to            find bases which are compatible to the KB called base.            Compatible means each is a module of the mixed base.        -   b. If we found two compatible mixed bases, then If the first            peak has a greater modulation than the second peak, add the            second peak onto the first peak as a secondary peak.            Otherwise, add the first peak onto the second peak as a            secondary peak. In either case, add them to the merged bases            list.        -   c. If we only found a single compatible base, then add it to            the merged base list.        -   d. If neither of these cases is true, then find the peak            with the greatest modulation. Add, if available, the peak            with the next greatest modulation to it as a secondary peak.            Add the peak to the merged peaks list.            Mixed-Base Variant Scoring

It is difficult to obtain his sensitivity and high rejection base on abasic morphological analysis of an electropherogram trace with a diverseset of traces and with the wide variety of phenomena that may beobserved. Specifically, it is hard to discriminate between “good” peaksand “bad” peaks because of the lack of absolute standards of such, andbecause the factors involved are myriad. Any such standard establishedfor pass and fail are subject to inaccuracies and cause either too mayrejections (false negatives) or too few rejections (false positives.)One approach is to utilize a training set to develop classifiers forapplying to traces, but the development of these classifiers isnon-trivial and the ability to validate coverage is a daunting task. Itis complicated due to nuances, which are difficult to automate.

The Solution

Multiple approaches are combined to solve the problem.

-   1.) Trace based metrics. A standard set of trace based metrics are    collected during processing. These metrics are basic such as peak    overlap, peak height, and modulation. These peak metrics provide a    common perspective into the morphology of the trace and form the    basis of our scoring.-   2.) Dual-Hypothesis. We consider the hypothesis that the KB Caller    has produced a correct interpretation of the electropherogram and    that its base call is correct, and we also consider the hypothesis    that instead the correct call is a match to the reference. The dual    hypothesis approach provides a differential signal which enables us    to discriminate between apparently good calls, apparently bad calls,    and indeterminable calls. That is, if the hypothesis for a match    with the KB Caller is strong and the match with the reference is    poor, then the call is good. If the match with the reference is good    and the match with the KB caller is poor, then the call is likely    bad. If both the KB Caller hypothesis and the Reference Hypothesis    are poor, then the call confidence is poor.-   3.) Other trace based metrics. In addition to the basic trace    metrics, we include recognition of specific defects which impact the    reliability of variant calling, such as end effects, stutter, and    peak spacing. These point out common characteristics that can be    scored.-   4.) Utilization of Pairing. We use pairing information, which    available to strengthen or refute variant calls. A pair is a forward    and reverse read taken from a single biological specimen. In    principle, it should lend identical base calls, however due to end    effects and primer effects, this is seldom the case. Still, when the    complementary read reinforces the call, the confidence is bolstered!    Variant Scoring Implementation    Calculation of Trace Based Metrics

The following trace based metrics comprise the Trace Based Metrics asdescribed below:

Squares Score

The purpose of the Squares Score is to compute metrics for the degree towhich the KB hypothesis is validated or refuted, and the degree to whichthe Reference hypothesis is validated or refuted based on overlaps withthe scoring peak. The Square Scores is a score of the expected pure baseor expected mixed-base. The Square Score validates the detection of theexpected base(s). Next, the Square Score computes a score based on theoverlap for both the KB hypothesis and also for the Referencehypothesis. The computation of overlap has been previously described inthe Trace Analysis section.

Error! Reference source not found. 26 illustrates the automation of thecomputation of the Square Score for a pure base assertion. The pure baseassertion may arise from computation of the KB Caller hypothesis or fromthe Reference Hypothesis. As shown in Error! Reference source not found.27 , overlap will lower the score once a (configurable) overlapthreshold has been reached. In the first case, there is limitedbackground noise but it is below the overlap threshold and the peakSquare Score would be high. In the second case, the intersection of asingle peak is far above the overlap threshold and so the Square Scorewould be low. This would occur in the case of a mixed-base that has beenincorrectly identified as a pure base. The third example show excessivebackground noise that challenges the pure base call. Because the overlapdue to the other traces is somewhat above overlap threshold, the SquareScore would be lowered.

As shown in FIG. 27, we have used a linear approach to score generationbased on peak overlap. The breakpoints are configurable and tunable toachieve the highest performance.

FIG. 28 illustrates the automation of the computation of the SquareScore for a mixed-base assertion. The mixed-base assertion could arisefrom computation of the KB Caller hypothesis but not from the ReferenceHypothesis as the reference sequence is pure-base. As shown in FIG. 29,appropriate overlap is required for a good Square Score.

For mixed bases, the overlap is computed for the expected secondary peakon the primary peak, and also for the overlap of the other peaks on thesecondary peak. If the overlap of the other peaks on the secondary peakexceeds a threshold, then we determine an interference score which willlower the Square Score outcome for the mixed-base assertion.

In the first case, there is clean overlap of the expected secondary peakon the primary peak. The Square Score would be high. In the second case,the intersection of a single peak is weak due to low amplitude and anoffset in displacement. Because the overlap is low, the Square Scorewould also be low. The third example shows excessive background noisethat challenges the pure base call. Because the overlap due to the othertraces is somewhat above overlap threshold, the Square Score would belowered.

As shown in FIG. 29, we have used a linear approach to Squares Scoregeneration based on peak overlap.

FIG. 30 shows the discrimination derived from Squares Score to rank truepositive and false positive outcomes. The graph is based on execution ofa large set of expertly curated data and shows good performance, with across over at a score around 7.5.

Amplitude Score

The Amplitude Score computes a score for the KB hypothesis and theReference hypothesis based on the amplitude of the scoring peak. Asillustrated in FIG. 31, in the upper red box, the height of the peakplays little role in discriminating good and bad peaks. All of thesepeaks are of the same quality. In the lower box, these peaks are noiseand cannot confidently contribute to a variant call. The Amplitude Scoreis consequently a qualifier of confidence rather and a continuousdiscriminator of good/bad variant confidence. A further note is that theTrace Analysis module has removed low-level peaks prior to scoring.

The amplitude score is based on parameters which are set during tuning.The score is computed as follows:

-   -   1.) For pure bases, the detection of the asserted pure-base peak        is validated. If the peak is not detected, a score of zero is        returned for both the KB hypothesis and for the reference        hypothesis. For mixed-bases the detection of both pure-base        modules is validated. If the peaks are not detected, a score of        zero is returned for both the KB hypothesis and for the        reference hypothesis.    -   2.) A mixed-base height ratio is compute if a secondary peak is        identified. In this case, the ratio of the heights of the        secondary to primary peak is computed. This height is converted        to a score based on a linear mapping similar to that described        in the Squares Score computation above.    -   3.) For pure bases, if the height of the primary peak falls        below a minimum height threshold the Amplitude Score for the KB        Caller and the reference hypothesis will both be set to zero.        Otherwise the score will be determined by a linear mapping        similar to that described for the Squares Score computation        above. The score is reduced by the mixed base ratio computed in        step 2.    -   4.) For mixed bases, the score for both modules is computed as        described in step 3. Each score is contingent on the mixed-base        score computed in step 2. The Amplitude Score is the lessor of        the two scores.

Error! Reference source not found. 32 provides an illustration (actualthresholds and slopes may vary) for amplitude score computation.

FIG. 33 illustrates the computation of the mixed-base ratio scoring(thresholds and slopes may vary.) The score is designed to provide hardlimits to rewards and benefits below and above certain thresholds, andto provide a linear range of reward/benefit in a short region between.

FIG. 34 shows the performance of the amplitude score in discriminatingtrue positive and false positive outcomes. As expected, the Amplitudescore has little impact on most of the points, as the outcomes are notpredicted by height. Discrimination of a small number of points is shownbetween amplitude scores of 0 and 1.

Modulation Score

The purpose of the Modulation Score is to compute metrics for the degreeto which the KB hypothesis is validated or refuted, and the degree towhich the Reference hypothesis is validated or refuted based on overlapswith the scoring peak. The Modulation Score is provided for the expectedpure base or expected mixed-base. The Modulation Score algorithmvalidates the detection of the expected base(s). Next, the ModulationScore algorithm computes a Modulation Score based on the degree ofmodulation for both the KB hypothesis and also for the Referencehypothesis. The computation of modulation has been previously describedin the Trace Analysis section.

FIG. 26 illustrates the mechanization of the computation of the SquareScore for a pure base assertion. The pure base assertion could arisefrom computation of the KB Caller hypothesis or from the ReferenceHypothesis. As shown in FIG. 27, overlap will lower the score once a(configurable) overlap threshold has been reached. In the first case,there is limited background noise but it is below the overlap thresholdand the peak Square Score would be high. In the second case, theintersection of a single peak is far above the overlap threshold and sothe Square Score would be low. This would occur in the case of amixed-base that has been incorrectly identified as a pure base. Thethird example show excessive background noise that challenges the purebase call. Because the overlap due to the other traces is somewhat aboveoverlap threshold, the Square Score would be lowered.

FIG. 35 shows the difference between modulation and amplitude and thedegree to which signals can be reliably detected at high amplitudes andlower modulation versus lower amplitudes, which require highermodulation. In this figure, all the signals can be reliably captured andshould not have any differential in reward/benefit.

The Modulation Score is based on parameters which are set during tuning.The score is computed as follows:

-   -   1.) For pure bases, the detection of the asserted pure-base peak        is validated. If the peak is not detected, a score of zero is        returned for both the KB hypothesis and for the reference        hypothesis. For mixed-bases the detection of both pure-base        modules is validated. If the peaks are not detected, a score of        zero is returned for both the KB hypothesis and for the        reference hypothesis.    -   2.) A mixed-base height ratio is compute if a secondary peak is        identified as previously describe in the Amplitude Score        computation.    -   3.) For pure bases, if the modulation of the primary peak falls        below a minimum threshold the Modulation Score for the KB Caller        and the reference hypothesis will both be set to zero. Otherwise        the Modulation Score will be determined by a linear mapping        similar to that described for the Squares Score computation        above. The score is reduced by the mixed base ratio computed in        step 2.    -   4.) For mixed bases, the Modulation Score for both modules is        computed as described in step 3. Each Modulation Score is        contingent on the mixed-base score computed in step 2. The        Modulation Score is the lessor of the two scores.

Error! Reference source not found. 36 shows the discrimination derivedfrom the modulation score (PTV) to rank true positive and false positiveoutcomes. The graph is based on execution of a large set of expertlycurated data and shows good performance, with a cross over at a scorearound 7.5.

Dual Hypothesis Score

The above metrics are combined into a single metric for both the KBHypothesis and the Reference Hypothesis as described following:Effective Squares Score=min(Square Score,1.0)*Squares Score FactorEffective Amplitude Score=min(Amplitude Score,1.0)*Amplitude ScoreFactorEffective Modulation Score=min(Modulation Score,1.0)*Modulation ScoreFactor

For both the KB Hypothesis score and the Reference Hypothesis score,these factors are combined as follows:Hypothesis Score=(Effective Squares Score+Effective AmplitudeScore+Effective Modulation Score)/3Trace Based Metrics Application

The Trace Based Metrics are utilized as a module of the variant scoredifferently for insertions, mismatches, and deletions.

-   -   1.) For mismatch variants, the KB hypothesis score and the        reference hypothesis scores are the computed as previously        described and carried forward into variant scoring.    -   2.) For insertion variants, the process follows from step 1        however the reference hypothesis score is always zero, as there        is no reference module to consider.    -   3.) For deletion variants, the KB hypothesis score and the        reference hypothesis score is computed as follows for the two        points surrounding the location of the deletion and the average        of these scores is passed forward. In the case of a missing base        prior to or following the point of deletion, then the scores for        the remaining base is carried forward. Deletions are further        examined for missed bases. If a base has been missed, then the        KB hypothesis score and the reference hypothesis score will be        set to zero.

Missed bases are computed as follows:

-   -   1.) The query position sequence reflected in the Peak Record        Database is examined to identify gaps in sequence. Should such a        gap exist, then a missed base has occurred.    -   2.) If no such gap has occurred, the then between the peak        before and after the considered peak, the trace distance is        contemplated. If this distance exceeds a threshold, a missed        base has occurred.        Combined Hypothesis Score

It is desirable to compute a single trace based hypothesis score tosubsequently use in variant scoring. The combined hypothesis score iscomputed differently for mismatches, insertions, and deletions asfollows:

-   1.) For mismatch variants, the combined hypothesis score is computed    as follows:    Combined Hypothesis Score=min(max(KB Hypothesis Score−Reference    Hypothesis Score,0),1)-   2.) For insertion variants, the combined hypothesis score is    computed as follows:    Combined Hypothesis Score=min(KB Hypothesis Score,1)-   3.) For deletion variants, the combined hypothesis score is computed    as follows:    If both the KB Hypothesis score and the Reference Hypothesis score    are zero, then the combined hypothesis score is zero, otherwise    compute:

Hypothesis  Difference = min (max (KB  Hypothesis  Score − Ref  Hypothesis  Score, 0)1)$\mspace{20mu}{{{Hypothesis}\mspace{14mu}{Avg}} = \frac{\left( {{{KB}\mspace{14mu}{Hypothesis}\mspace{14mu}{Score}} + \mspace{11mu}{{Ref}\mspace{14mu}{Hypothesis}\mspace{14mu}{Score}}} \right)}{2}}$Combined  Hypothesis  Score = (1 − Hypothesis  Difference) * Hypothesis  AverageOther Trace Based ScoresStutter Penalty

The stutter score is computed as described in the Trace Analysissection. The Stutter Penalty is computed as follows:

When stutter is associated in the trace, but not detected in the peak,the stutter penalty is computed as follows:Stutter Penalty=(1.0−Stutter Score)*0.5

When stutter is detected in the scoring peak, the stutter score iscomputed as follows:Stutter Penalty=1.0−Stutter Score

When no stutter is detected, the stutter penalty is set to 1.0.

End Score

Low quality base calls occur on the ends of virtually every Sanger readand must be removed by quality trimming to avoid incorrect variantcalling. The quality trimming algorithm seeks a window (˜20 bases) witha limited number of low quality bases (<4) within that window to definethe clear range that should be algorithmically processed into variantcalls. This quality trimming approach frequently incorporates a few lowquality base calls in the clear range. This is undesirable when theycause false variant calls. Sometimes this approach includes just a fewlow quality base calls in the interior of the window, and this isdesirable when it causes no harm and extends high-quality sequencebefore it. The algorithm's trace analysis is biased towards achievingconcurrence with the KB called bases, and cannot be fully relied on toeliminate false positives that rise from included low-quality data onthe ends. The following approach mitigates calling of false variantsfrom low-quality base calls on the ends of reads.

Low-quality base calls may occur on the end of a read and which may giverise to false positive outcomes. Particularly as these portions of thereads tend to be unpaired, special processing is justified to avoid thefalse calls.

The End Score algorithm is implemented as follows:

Variants which occur within the region of the trace overlapping with thetrimming window (typically 20 bases from the KB Call reference frame andextending into the clear range) are examined. The processing formismatch and insertion variants is different than that for deletionvariants.

For mismatch and insertion variants,

-   1.) The QV value produced by KB caller is examined for the peak of    the called variant.-   2.) If the QV value is below a certain threshold depending if the    variant is pure-base or mixed-base, then a punishment is computed.-   3.) The punishment is the ratio of the QV value and the threshold.-   4.) The End Score is the greater of the maximum end-score penalty    and the ratio.

For deletion variants,

-   1.) The QV value produced by KB caller is examined for the peak    preceding and following the called variant.-   2.) If the QV value is below a certain threshold depending if the    variant is pure-base or mixed-base, then a punishment is computed.-   3.) The punishment is the ratio of the QV value and the threshold.-   4.) The End Score is the greater of the maximum end-score penalty    and the ratio.    Low Modulation Score

The low modulation score is computed for each peak in the trace regionas previously described in the Trace Analysis. The Low Modulation Scoreis computed differentially for mismatches and insertions and fordeletion variants as follows:

-   1.) For mismatches and insertion variants, the low modulation score    is the reported low modulation score.-   2.) For deletion variants, the low modulation score is the average    of the reported low modulation scores of the peak proceeding and the    peak following the point of the deletion.    Combined Trace Score

It is desirable to produce a final combined trace score for input intovariant scoring. The combined trace score is computed as follows:Combined Trace Score=Combined Hypothesis Score*End Score*Stutter Penalty*Low Modulation ScoreConcordance Score

The end user is able to aggregate samples into groups, which areexperimental data produced from the same genomic material. These datacould be provided by running forward and reverse assays for the samesample, or running multiple assays using different equipment or analysissettings. These samples provide a powerful mechanism that providesredundant observations to reinforce the trace analysis.

The concordance score is implemented as follows:

-   1.) For each variant observation, create a background population.    That is a list of the imported reads which are in the same sample    group, and whose clear range overlaps with the variant position.-   2.) Screen the background to identify complementary reads. That is,    if the variant is observed on a forward trace, only the reverse    (complementary) traces can contribute to the concordance score.    Likewise, if the variant is observed on a reverse trace, only the    forward traces can contribute to the concordance score.-   3.) For each relevant background read in an insertion and deletion    variant:    -   a. if the considered trace has no variant observation at the        corresponding location, then increment the number of refuting        observations,    -   b. Otherwise if it has an identical observation increment the        number of confirming observations.    -   c. Compute the concordance score as:

${{Concordance}\mspace{14mu}{Score}} = \frac{{number}\mspace{14mu}{of}\mspace{14mu}{confirmations}}{\left( {{{number}\mspace{20mu}{of}\mspace{14mu}{confirmations}} + \mspace{40mu}{{number}\mspace{14mu}{of}\mspace{14mu}{refutes}}} \right)}$

-   4.) For each relevant background read in a mismatch variant:    -   a. Attempt to reference the peak in the corresponding variant        position from the background sequence.    -   b. If a corresponding peak cannot be retrieved, return a score        of 0.5 (neutral.)    -   c. Confirm that the corresponding peak is compatible with the        variant peak, that is for a pure base, it has the same peak        detection and for a mixed-base it has the same two        primary/secondary peak detections.    -   d. If the corresponding peak is not compatible with the variant        peak, return 0.0 (strong refutation.)    -   e. Compute the concordance score as described below.        Compute Concordance Background Population

The background is created as follows:

-   1.) Consider all the reads which are in the same read group.-   2.) Exclude the subject variant from the background population-   3.) Ensure that the read is aligned with a passing quality-   4.) Ensure that the read spans the region of the variant-   5.) If the read includes an identical variant, add the variant to    the background population.-   6.) Otherwise, create a background variant, perform Trace Analysis    on that variant, and add it to the background population.    Compute Mismatch Variant Concordance Score

The concordance score for mismatch variants is derived from traceanalysis. The stringency applied for concordance is adjusted to be morespeculative than the scoring tests applied previously.

The mismatch variant concordance score is computed as follows:

-   1.) Confirm that the corresponding peak is compatible with the    variant peak; that is for a pure base, it has the same peak    detection and for a mixed-base it has the same two primary/secondary    peak detections.-   2.) If the variant peak is pure:    -   a. If the background peak's primary peak matches the variant        peak, compute the concordance score from the squares score based        on a linear mapping.    -   b. Otherwise, if the background peak's secondary peak matches        the variant peak then compute the concordance score from the        secondary peak's squares score based on a linear mapping.    -   c. Otherwise, compute the height and slope of the corresponding        trace around the peak location. If the height of the peak's        corresponding trace at the peak location is too low, return a        concordance score of 0. If the slope is not strongly negative,        then return a concordance score of 0. Otherwise, compute a        concordance score based on the height of the peak using a linear        mapping.-   3.) If the variant peak is mixed:    -   a. If the background peaks' primary and secondary bases match        the variant peaks' primary and secondary bases, then compute the        concordance score based on a linear mapping of the squares score        for the background peak.    -   b. If both peaks were found (but they were not primary and        secondary) compute the concordance score based on the overlap of        those peaks, using a linear mapping.    -   c. If either peak, or both peaks were not found, compute the        concordance scores as describe above in step 2c.        Compute Variant Score

For each variant, the variant score is computed from the trace score andthe concordance score as follows. Note that the concordance score caneither strengthen or weaken the results of the trace score to a degreeproportional to the trace score and adjusted by a gain.Effective Trace Score=Trace Score*Trace Score GainEffective Concordance Score=(Concordance Score−Concordance ScoreBias)*(Effective Trace Score*Concordance Score Gain)Variant Score=min(max(Trace Score+Concordance Score,0.0)1.0)

Error! Reference source not found. 37 shows the performance of thevariant scoring to discriminate true positive and false positiveoutcomes. The performance provides a range of adjustments to the user toenhance detection and to enhance rejection.

Computer-Implemented System

Those skilled in the art will recognize that the operations of thevarious embodiments may be implemented using hardware, software,firmware, or combinations thereof, as appropriate. For example, someprocesses can be carried out using processors or other digital circuitryunder the control of software, firmware, or hard-wired logic. (The term“logic” herein refers to fixed hardware, programmable logic and/or anappropriate combination thereof, as would be recognized by one skilledin the art to carry out the recited functions.) Software and firmwarecan be stored on non-transitory computer-readable media. Some otherprocesses can be implemented using analog circuitry, as is well known toone of ordinary skill in the art. Additionally, memory or other storage,as well as communication modules, may be employed in embodiments of theinvention.

FIG. 38 is a block diagram that illustrates a computer system 3800 thatmay be employed to carry out processing functionality, according tovarious embodiments. Instruments to perform experiments may be connectedto the exemplary computing system 3800. Computing system 3800 caninclude one or more processors, such as a processor 3804. Processor 3804can be implemented using a general or special purpose processing enginesuch as, for example, a microprocessor, controller or other controllogic. In this example, processor 3804 is connected to a bus 3802 orother communication medium.

Further, it should be appreciated that a computing system 3800 of FIG.38 may be embodied in any of a number of forms, such as a rack-mountedcomputer, mainframe, supercomputer, server, client, a desktop computer,a laptop computer, a tablet computer, hand-held computing device (e.g.,PDA, cell phone, smart phone, palmtop, etc.), cluster grid, netbook,embedded systems, or any other type of special or general purposecomputing device as may be desirable or appropriate for a givenapplication or environment. Additionally, a computing system 3800 caninclude a conventional network system including a client/serverenvironment and one or more database servers, or integration withLIS/LIMS infrastructure. A number of conventional network systems,including a local area network (LAN) or a wide area network (WAN), andincluding wireless and/or wired modules, are known in the art.Additionally, client/server environments, database servers, and networksare well documented in the art. According to various embodimentsdescribed herein, computing system 3800 may be configured to connect toone or more servers in a distributed network. Computing system 3800 mayreceive information or updates from the distributed network. Computingsystem 3800 may also transmit information to be stored within thedistributed network that may be accessed by other clients connected tothe distributed network.

Computing system 3800 may include bus 3802 or other communicationmechanism for communicating information, and processor 3804 coupled withbus 3802 for processing information.

Computing system 3800 also includes a memory 3806, which can be a randomaccess memory (RAM) or other dynamic memory, coupled to bus 3802 forstoring instructions to be executed by processor 3804. Memory 3806 alsomay be used for storing temporary variables or other intermediateinformation during execution of instructions to be executed by processor3804. Computing system 3800 further includes a read only memory (ROM)3808 or other static storage device coupled to bus 3802 for storingstatic information and instructions for processor 3804.

Computing system 3800 may also include a storage device 3810, such as amagnetic disk, optical disk, or solid state drive (SSD) is provided andcoupled to bus 3802 for storing information and instructions. Storagedevice 3810 may include a media drive and a removable storage interface.A media drive may include a drive or other mechanism to support fixed orremovable storage media, such as a hard disk drive, a floppy disk drive,a magnetic tape drive, an optical disk drive, a CD or DVD drive (R orRW), flash drive, or other removable or fixed media drive. As theseexamples illustrate, the storage media may include a computer-readablestorage medium having stored therein particular computer software,instructions, or data.

In alternative embodiments, storage device 3810 may include othersimilar instrumentalities for allowing computer programs or otherinstructions or data to be loaded into computing system 3800. Suchinstrumentalities may include, for example, a removable storage unit andan interface, such as a program cartridge and cartridge interface, aremovable memory (for example, a flash memory or other removable memorymodule) and memory slot, and other removable storage units andinterfaces that allow software and data to be transferred from thestorage device 3810 to computing system 3800.

Computing system 3800 can also include a communications interface 3818.Communications interface 3818 can be used to allow software and data tobe transferred between computing system 3800 and external devices.Examples of communications interface 3818 can include a modem, a networkinterface (such as an Ethernet or other NIC card), a communications port(such as for example, a USB port, a RS-232C serial port), a PCMCIA slotand card, Bluetooth, etc. Software and data transferred viacommunications interface 3818 are in the form of signals which can beelectronic, electromagnetic, optical or other signals capable of beingreceived by communications interface 3818. These signals may betransmitted and received by communications interface 3818 via a channelsuch as a wireless medium, wire or cable, fiber optics, or othercommunications medium. Some examples of a channel include a phone line,a cellular phone link, an RF link, a network interface, a local or widearea network, and other communications channels.

Computing system 3800 may be coupled via bus 3802 to a display 3812,such as a cathode ray tube (CRT) or liquid crystal display (LCD), fordisplaying information to a computer user. An input device 3814,including alphanumeric and other keys, is coupled to bus 3802 forcommunicating information and command selections to processor 3804, forexample. An input device may also be a display, such as an LCD display,configured with touchscreen input capabilities. Another type of userinput device is cursor control 3816, such as a mouse, a trackball orcursor direction keys for communicating direction information andcommand selections to processor 3804 and for controlling cursor movementon display 3812. This input device typically has two degrees of freedomin two axes, a first axis (e.g., x) and a second axis (e.g., y), thatallows the device to specify positions in a plane. A computing system3800 provides data processing and provides a level of confidence forsuch data. Consistent with certain implementations of embodiments of thepresent teachings, data processing and confidence values are provided bycomputing system 3800 in response to processor 3804 executing one ormore sequences of one or more instructions contained in memory 3806.Such instructions may be read into memory 3806 from anothercomputer-readable medium, such as storage device 3810. Execution of thesequences of instructions contained in memory 3806 causes processor 3804to perform the process states described herein. Alternatively hard-wiredcircuitry may be used in place of or in combination with softwareinstructions to implement embodiments of the present teachings. Thusimplementations of embodiments of the present teachings are not limitedto any specific combination of hardware circuitry and software.

The term “computer-readable medium” and “computer program product” asused herein generally refers to any media that is involved in providingone or more sequences or one or more instructions to processor 3804 forexecution. Such instructions, generally referred to as “computer programcode” (which may be grouped in the form of computer programs or othergroupings), when executed, enable the computing system 3800 to performfeatures or functions of embodiments of the present invention. These andother forms of non-transitory computer-readable media may take manyforms, including but not limited to, non-volatile media, volatile media,and transmission media. Non-volatile media includes, for example, solidstate, optical or magnetic disks, such as storage device 3810. Volatilemedia includes dynamic memory, such as memory 3806. Transmission mediaincludes coaxial cables, copper wire, and fiber optics, including thewires that comprise bus 3802.

Common forms of computer-readable media include, for example, a floppydisk, a flexible disk, hard disk, magnetic tape, or any other magneticmedium, a CD-ROM, any other optical medium, punch cards, paper tape, anyother physical medium with patterns of holes, a RAM, PROM, and EPROM, aFLASH-EPROM, any other memory chip or cartridge, a carrier wave asdescribed hereinafter, or any other medium from which a computer canread.

Various forms of computer readable media may be involved in carrying oneor more sequences of one or more instructions to processor 3804 forexecution. For example, the instructions may initially be carried onmagnetic disk of a remote computer. The remote computer can load theinstructions into its dynamic memory and send the instructions over atelephone line using a modem. A modem local to computing system 3800 canreceive the data on the telephone line and use an infra-red transmitterto convert the data to an infra-red signal. An infra-red detectorcoupled to bus 3802 can receive the data carried in the infra-red signaland place the data on bus 3802. Bus 3802 carries the data to memory3806, from which processor 3804 retrieves and executes the instructions.The instructions received by memory 3806 may optionally be stored onstorage device 3810 either before or after execution by processor 3804.

It will be appreciated that, for clarity purposes, the above descriptionhas described embodiments of the invention with reference to differentfunctional units and processors. However, it will be apparent that anysuitable distribution of functionality between different functionalunits, processors or domains may be used without detracting from theinvention. For example, functionality illustrated to be performed byseparate processors or controllers may be performed by the sameprocessor or controller. Hence, references to specific functional unitsare only to be seen as references to suitable means for providing thedescribed functionality, rather than indicative of a strict logical orphysical structure or organization.

Distributed System

Some of the elements of a typical Internet network configuration 600 areshown in FIG. 39, wherein a number of client machines 3902 possibly in aremote local office, are shown connected to agateway/hub/tunnel-server/etc 3910 which is itself connected to theinternet 3908 via some internet service provider (ISP) connection 3910.Also shown are other possible clients 3912 similarly connected to theinternet 3908 via an ISP connection 3914, with these units communicatingto possibly a central lab or office, for example, via an ISP connection3916 to a gateway/tunnel-server 3918 which is connected 3920 to variousenterprise application servers 3922 which could be connected throughanother hub/router 3926 to various local clients 3930. Any of theseservers 3922 could function as a development server for the analysis ofpotential content management and delivery design solutions as describedin the present invention, as more fully described below.

Although various embodiments have been described with respect to certainexemplary embodiments, examples, and applications, it will be apparentto those skilled in the art that various modifications and changes maybe made without departing from the present teachings.

What is claimed is:
 1. A method for detecting nucleic acid sequencevariants in electropherogram data produced by nucleic acid sequencing,the method comprising: receiving electropherogram data comprising one ormore nucleic acid sequences from an instrument wherein the nucleic acidsequences are imported into one or more query sequence records and arevalidated using a translation table as indicating one or more valid purebases or one or more valid mixed bases; analyzing the electropherogramdata to identify mixed bases in the electropherogram data includingdetecting an orientation of each of the one or more nucleic acidsequences and identifying a best it mixed-base alignment between thequery sequence record and a reference sequence record; identifyingfeatures within the electropherogram data indicative of errors whereinan error is indicated where one or more sequence features do not fallwithin an acceptable range or where an alignment level between the querysequence record and the reference sequence record does not fall withinan acceptable range; validating the identified mixed base by importinganalyzed trace data and extracting peak location data for each of fourelectropherogram channels; and determining variants in theelectropherogram data based on detecting one or more peaks in theelectropherogram data for the validated mixed bases.
 2. The method ofclaim 1, wherein analyzing the electropherograni data to identify mixedbases includes determining a mixed-base alignment.
 3. The method ofclaim 1, wherein validating the identified mixed bases comprises:detecting peaks in the electropherogram data; detecting intersections inthe electropherogram data; and detecting stutter peaks in theelectropherogram data.
 4. The method of claim 3, wherein validating theidentified mixed bases further comprises: mapping the detected peaks. 5.The method of claim 3, wherein validating the identified mixed basesfurther comprises: merging the peaks based on the detected peaks; thedetected intersections, and the detected stutter peaks.
 6. The method ofclaim 1, further comprising: validating the determined variants based ongenerating a score based on the identified features.
 7. A system fordetecting variants in electropherogram data produced by nucleic acidsequencing, the system comprising: an input module configured to receiveelectropherogram data comprising one or more nucleic acid sequences froman instrument wherein the nucleic acid sequences are imported into oneor more query sequence records and are validated using a basetranslation table as indicating one or more valid pure bases or one ormore valid mixed bases; a mixed base variant validator module toidentify mixed bases in the electropherogram data including detecting anorientation of each of the one or more nucleic acid sequences andidentifying a best fit mixed-base alignment between the query sequencerecord and a reference sequence record, identify features within theelectropherogram data indicative of errors wherein an error is indicatedwhere one or more sequence features do not fall within an acceptablerange or where an alignment level between the query sequence record andthe reference sequence record does not fall within an acceptable range,and validate the identified mixed bases by importing analyzed trace dataand extracting peak location data for each of four electropherogramchannels; and a variant caller configured to determine variants in theelectropherogram data based on detecting one or more peaks in theelectropherogram data for the validated mixed bases.
 8. The system ofclaim 7, further comprising: an alignment module configured to analyzethe electropherogram data to determine a mixed-base alignment.
 9. Thesystem of claim 7, further comprising: a stutter and peak detectorconfigured to identify features within the electropherogram dataindicative of errors.
 10. The system of claim 7, further comprising: avariant score generator configured to validate variants in theelectropherogram data.
 11. A computer-readable storage medium encodedwith processor executable instructions for detecting nucleic acidsequence variants in electropherogram data produced by nucleic acidsequencing, the instructions comprising instructions for: receivingelectropherogram data comprising one or more nucleic acid sequences froman instrument wherein the nucleic acid sequences are imported into oneor more query sequence records and are validated using a basetranslation table as indicatingnne or more valid pure bases or one ormore valid mixed bases: analyzing the electropherogram data to identifymixed bases in the electropherogram data including detecting anorientation of each of the one or more nucleic acid sequences andidentifying a best fit mixed-base alignment between the query sequencerecord and a reference sequence record; identifying features within theelectropherogram data indicative of errors, wherein an error isindicated where one or more sequence features do not fall within anacceptable range or where an alignment level between the query sequencerecord and the reference sequence record does not fall within anacceptable range; validating the identified mixed bases by importinganalyzed trace data and extracting peak location data for each of fourelectropherogram channels; and determining variants in theelectropherogram data based on detective one or more peaks in theelectropherogram data for the validated mixed bases.
 12. The method ofclaim 11, wherein analyzing the electropherogram data to identify mixedbases includes determining a mixed-base alignment.
 13. The method ofclaim 11, wherein validating the identified mixed bases comprises:detecting peaks in the electropherogram data; detecting intersections inthe electropherogram data; and detecting stutter peaks in theelectropherogram data.
 14. The computer-readable storage medium of claim13, wherein the instructions for validating the identified mixed basesfurther comprises instructions for: mapping the detected peaks.
 15. Thecomputer-readable storage medium of claim 13, wherein the instructionsfor validating the identified mixed bases further comprises instructionsfor: merging the peaks based on the detected peaks, the detectedintersections, and the detected stutter peaks.
 16. The computer-readablestorage medium of claim 11, further comprising instructions for:validating the determined variants based on generating a score based onthe identified features.